This file contains all data manipulations, analyses, and visualizations used to produce the temperature, calcification, and survival results in Castillo KD, Bove CB, et al. (In Prep). All gene expression data and analyses can be found in this repository on the RT_Host_Sym_GE.R script and the ITS2 analyses can be found in the reciprocal_transplants_ITS2.Rmd file.

In situ temperature

Overall temperatures

Mean +/- SE and distribution across reefs

reef Mean SD Min Max N SE
Nearshore 29.1 1.66 25.5 33.3 16088 0.0130875
Backreef 28.7 1.61 24.6 32.5 16088 0.0126933
Forereef 28.5 1.42 25.2 31.6 16088 0.0111953


Mean temperatures

Means (monthly, weekly, daily)


Temperature ranges

Ranges (monthly, weekly, daily)



Coral survival

Figure 2A


Data Visualization

Figure 2A. Fraction of surviving Siderastrea siderea colonies through time (2011-2015) after reciprocal transplantation with respect to source location and transplanted location. Source location is represented by line type (FR = dashed; BR = solid; NS = dotted) and transplant location is denoted by color (orange = NS [nearshore], green = BR [backreef], and blue = FR [forereef]).


Supplementary Tables

Supplemental Table 4

Table S4. Number or corals surviving per year in each transplant location (BR = backreef, FR = forereef, NS = Nearshore).

Source Transplant 2011 2012 2013 2014 2015
BR BR 6 6 6 6 6
BR FR 6 6 6 5 5
BR NS 6 4 3 3 3
FR BR 6 6 6 6 6
FR FR 6 6 6 6 6
FR NS 6 3 2 2 2
NS BR 6 6 6 6 6
NS FR 6 6 6 6 6
NS NS 6 5 4 4 4


Supplemental Table 5

sur$Source <- fct_relevel(sur$Source, c("FR", "BR", "NS"))
sur$Transplant <- fct_relevel(sur$Transplant, c("FR", "BR", "NS"))

surv.mod <- coxph(sur.r ~ Transplant + Source, data = sur)


Table S5. Statistical assessment of the cox proportional hazards survival model. (A) Type 2 analysis of deviance of the overall effect of transplant and source. (B) Cox proportional hazard model output, with exp(coef) representing the hazard ratio, se(coef) is the standard error, z is the z score, and Pr(>|z|) is the probability that the estimate could be 0.

LR Chisq Df Pr(>Chisq)
Transplant 19.831 2 4.94e-05
Source 1.622 2 4.44e-01
coefficient exp(coef) se(coef) z Pr(>|z|)
TransplantBR -18.88 0.00 12566.10 0.00 1.00
TransplantNS 2.58 13.25 1.06 2.44 0.01
SourceBR -0.17 0.85 0.71 -0.23 0.81
SourceNS -1.00 0.37 0.87 -1.15 0.25


Calcification rate


Overall Calcification Statistics

Model selection

Overall calcification Akaike information criterion (AIC) model selection Model selection for assessment of source and transplant location impacts on overall (2012 - 2015) coral calcification rates was performed using AIC. The model with the lowest AIC (in bold) best fit the data and was used for analyses.
df AIC
Source * Transplant 10 -15.05
Source + Transplant 6 -8.51
Transplant only 4 -7.76
Source only 4 -12.34


Modelling Parametric Bootstrap 95% Confidence Intervals

Model:

calc.model <- lm(rate ~ source * trans, data = RT.calc.fin) # selected model


Modeled Mean Calcification Rate and 95% Confidence Interval

Parametric bootstrapped mean and 95% confidence intervals of calcification rates (mg cm-2 day-1) in response to transplant treatment (BR = backreef, FR = forereef, NS = Nearshore).
Treatment Modeled Mean Lower 95% CI Upper 95% CI
BR to BR 0.68 0.52 0.85
BR to FR 0.64 0.45 0.83
BR to NS 0.88 0.64 1.11
FR to BR 1.00 0.83 1.16
FR to FR 0.91 0.78 1.04
FR to NS 0.56 0.32 0.80
NS to BR 0.74 0.58 0.91
NS to FR 0.76 0.61 0.90
NS to NS 0.88 0.72 1.04

Figure 2B

Figure 2B. Calcification rate (mg cm–2 day–1) averaged over the entire transplant experimental period (2012 – 2015) by transplant location. Source location is represented by color: orange = NS (nearshore), green = BR (backreef), and blue = FR (forereef). Colored bars represent modeled 95% confidence intervals with corresponding raw calcification rates per colony denoted by circles of the same color.


Calcification by Year

Model selection

Year calcification Akaike information criterion (AIC) model selection

Model selection for assessment of source and transplant location impacts on Year coral calcification rates was performed using AIC. The model in bold appropriately fit the data and was used for analyses.
df AIC
Source * Transplant * Year 28 6.48
Source + Transplant + Year 8 19.38
Source * Transplant + Year 12 10.25
Source * Year + Transplant 12 24.21
Transplant * Year + Source 12 6.24
Transplant only 4 67.55
Source only 4 61.23
Year only 4 19.68


Modelling Parametric Bootstrap 95% Confidence Intervals

Model:

tp.model <- lm(rate ~ source * trans * TP, data = RT.calc.tp) # selected model


Modeled Mean Calcification Rate and 95% Confidence Interval by Year

Parametric bootstrapped mean and 95% confidence intervals of calcification rates (mg cm-2 day-1) in response to transplant treatment (BR = backreef, FR = forereef, NS = Nearshore) over time.
Treatment Modeled Mean Lower 95% CI Upper 95% CI
BR to BR in 2013 0.53 0.35 0.71
BR to BR in 2014 0.61 0.43 0.79
BR to BR in 2015 0.96 0.74 1.17
BR to FR in 2013 0.58 0.36 0.80
BR to FR in 2014 0.41 0.18 0.63
BR to FR in 2015 0.93 0.67 1.18
BR to NS in 2013 0.57 0.34 0.78
BR to NS in 2014 0.62 0.32 0.93
BR to NS in 2015 1.48 1.18 1.80
FR to BR in 2013 0.78 0.60 0.95
FR to BR in 2014 0.83 0.65 1.01
FR to BR in 2015 1.26 1.05 1.48
FR to FR in 2013 0.99 0.82 1.17
FR to FR in 2014 0.70 0.53 0.88
FR to FR in 2015 1.05 0.86 1.23
FR to NS in 2013 0.52 0.26 0.78
FR to NS in 2014 0.25 -0.06 0.57
FR to NS in 2015 0.99 0.67 1.29
NS to BR in 2013 0.59 0.39 0.79
NS to BR in 2014 0.76 0.57 0.96
NS to BR in 2015 0.92 0.70 1.13
NS to FR in 2013 0.79 0.61 0.96
NS to FR in 2014 0.67 0.49 0.86
NS to FR in 2015 0.84 0.62 1.05
NS to NS in 2013 0.73 0.50 0.95
NS to NS in 2014 0.59 0.38 0.80
NS to NS in 2015 1.33 1.12 1.55

Data Visualization

Figure S2A | Calcification rate (mg cm-2 day-1) at yearly intervals over the entire transplant experimental period (2012 – 2015) by source location. Transplant location is represented by color: red = NS (nearshore), green = BR (backreef), and blue = FR (forereef). Colored bars represent modeled 95% confidence intervals with corresponding raw calcification rates per colony denoted by circles of the same color.


Supplemental Tables

Supplemental Table 1

Table S1. Akaike information criterion (AIC) model selection for calcification linear models. Model selection for assessment of source and transplant location impacts on overall (2012 - 2015) and annual coral calcification rates performed using AIC. The model with the lowest AIC (in bold) best fit the data and was used for analyses.

df AIC
Overall Calcification
Source * Transplant 10 -15.05
Source + Transplant 6 -8.51
Transplant only 4 -7.76
Source only 4 -12.34
Annual Calcification
Source * Transplant * Year 28 6.48
Source + Transplant + Year 8 19.38
Source * Transplant + Year 12 10.25
Source * Year + Transplant 12 24.21
Transplant * Year + Source 12 6.24
Transplant only 4 67.55
Source only 4 61.23
Year only 4 19.68


Supplemental Table 6

Table S6 Linear model output assessing overall calcification responses. The intercept was set at corals from the backreef (BR) transplanted back to the backreef.

Estimate Std. Error t value Pr(>|t|)
(Intercept) 0.68 0.08 8.10 0.00
source (FR) 0.32 0.12 2.65 0.01
source (NS) 0.06 0.12 0.49 0.63
transplant (FR) -0.05 0.13 -0.37 0.72
transplant (NS) 0.19 0.15 1.33 0.20
source (FR):transplant (FR) -0.04 0.17 -0.22 0.83
source (NS):transplant (FR) 0.07 0.17 0.38 0.71
source (FR):transplant (NS) -0.63 0.21 -3.03 0.01
source (NS):transplant (NS) -0.05 0.19 -0.28 0.78


Supplemental Table 7

Table S7. Modeled mean calcification rate and 95% confidence interval. Parametric bootstrapped mean and 95% confidence intervals of calcification rates (mg cm-2 day-1) in response to transplant treatment (BR = backreef, FR = forereef, NS = Nearshore).

Treatment Modeled Mean Lower 95% CI Upper 95% CI
BR to BR 0.68 0.52 0.85
BR to FR 0.64 0.45 0.83
BR to NS 0.88 0.64 1.11
FR to BR 1.00 0.83 1.16
FR to FR 0.91 0.78 1.04
FR to NS 0.56 0.32 0.80
NS to BR 0.74 0.58 0.91
NS to FR 0.76 0.61 0.90
NS to NS 0.88 0.72 1.04


Supplemental Table 8

Table S8 Linear model output assessing annual calcification responses. The intercept was set at corals from the backreef (BR) transplanted back to the backreef from 2013.

Estimate Std. Error t value Pr(>|t|)
(Intercept) 0.53 0.09 5.79 0.00
source (FR) 0.25 0.13 1.94 0.06
source (NS) 0.06 0.14 0.44 0.66
transplant (FR) 0.05 0.14 0.34 0.74
transplant (NS) 0.04 0.14 0.27 0.78
Year (2014) 0.08 0.13 0.63 0.53
Year (2015) 0.43 0.14 2.98 0.00
source (FR):transplant (FR) 0.16 0.19 0.85 0.40
source (NS):transplant (FR) 0.15 0.20 0.75 0.45
source (FR):transplant (NS) -0.30 0.21 -1.40 0.17
source (NS):transplant (NS) 0.10 0.21 0.50 0.62
source (FR):Year (2014) -0.03 0.18 -0.17 0.87
source (NS):Year (2014) 0.09 0.19 0.48 0.63
source (FR):Year (2015) 0.06 0.20 0.27 0.79
source (NS):Year (2015) -0.09 0.21 -0.44 0.66
transplant (FR):Year (2014) -0.25 0.20 -1.23 0.22
transplant (NS):Year (2014) -0.03 0.23 -0.13 0.90
transplant (FR):Year (2015) -0.08 0.22 -0.36 0.72
transplant (NS):Year (2015) 0.48 0.24 1.99 0.05
source (FR):transplant (FR):Year (2014) -0.09 0.27 -0.32 0.75
source (NS):transplant (FR):Year (2014) -0.03 0.28 -0.11 0.91
source (FR):transplant (NS):Year (2014) -0.28 0.34 -0.85 0.40
source (NS):transplant (NS):Year (2014) -0.28 0.31 -0.90 0.37
source (FR):transplant (FR):Year (2015) -0.35 0.30 -1.19 0.24
source (NS):transplant (FR):Year (2015) -0.20 0.31 -0.66 0.51
source (FR):transplant (NS):Year (2015) -0.50 0.35 -1.43 0.16
source (NS):transplant (NS):Year (2015) -0.22 0.32 -0.68 0.50


Supplemental Table 9

Table S9. Modeled mean calcification rate and 95% confidence interval by year. Parametric bootstrapped mean and 95% confidence intervals of calcification rates (mg cm-2 day-1) in response to transplant treatment (BR = backreef, FR = forereef, NS = Nearshore) over time.

Treatment Modeled Mean Lower 95% CI Upper 95% CI
BR to BR in 2013 0.53 0.35 0.71
BR to BR in 2014 0.61 0.43 0.79
BR to BR in 2015 0.96 0.74 1.17
BR to FR in 2013 0.58 0.36 0.80
BR to FR in 2014 0.41 0.18 0.63
BR to FR in 2015 0.93 0.67 1.18
BR to NS in 2013 0.57 0.34 0.78
BR to NS in 2014 0.62 0.32 0.93
BR to NS in 2015 1.48 1.18 1.80
FR to BR in 2013 0.78 0.60 0.95
FR to BR in 2014 0.83 0.65 1.01
FR to BR in 2015 1.26 1.05 1.48
FR to FR in 2013 0.99 0.82 1.17
FR to FR in 2014 0.70 0.53 0.88
FR to FR in 2015 1.05 0.86 1.23
FR to NS in 2013 0.52 0.26 0.78
FR to NS in 2014 0.25 -0.06 0.57
FR to NS in 2015 0.99 0.67 1.29
NS to BR in 2013 0.59 0.39 0.79
NS to BR in 2014 0.76 0.57 0.96
NS to BR in 2015 0.92 0.70 1.13
NS to FR in 2013 0.79 0.61 0.96
NS to FR in 2014 0.67 0.49 0.86
NS to FR in 2015 0.84 0.62 1.05
NS to NS in 2013 0.73 0.50 0.95
NS to NS in 2014 0.59 0.38 0.80
NS to NS in 2015 1.33 1.12 1.55


GE Plasticity Tables

Supplemental Table 3

(These model outputs are taken from the plasticity analysis and just constructed into tables here)

Table S3. Akaike information criterion (AIC) model selection for coral host and algal symbiont gene expression plasticity. Model selection for assessment of source and transplant location impacts on gene expression plasticity performed using AIC.

Host Model AIC BIC Nagelkerke’s R2
Source * Transplant 46.845 64.687 0.833
Source + Transplant 102.088 112.794 0.146
Transplant 99.632 106.769 0.108
Source 102.398 109.535 0.034
Symbiont Model AIC BIC Nagelkerke’s R2
Source * Transplant 31.742 46.714 0.863
Source + Transplant 94.949 104.930 0.038
Transplant 91.827 98.481 0.011
Source 91.317 97.971 0.027


Supplemental Table 10A

(These model outputs are taken from the plasticity analysis and just constructed into tables here)

Table S10A. Linear model output assessing coral host gene expression plasticity. The intercept was set at corals from the backreef transplanted back to the backreef. (BR = backreef, FR = forereef, NS = Nearshore)

Estimate Std. Error t value Pr(>t)
(Intercept) -0.6692 0.1731 -3.866 0.000460 ***
Source (FR) 1.1464 0.2448 4.683 4.17e-05 ***
Source (NS) 0.6369 0.2568 2.481 0.018072 *
Transplant (FR) 1.1503 0.2448 4.699 3.97e-05 ***
Transplant (NS) 0.0778 0.2998 0.259 0.796787
Source (FR):Transplant (FR) -3.0430 0.3462 -8.789 2.22e-10 ***
Source (NS):Transplant (FR) -0.2569 0.3548 -0.724 0.473857
Source (FR):Transplant (NS) 0.1188 0.4580 0.259 0.796844
Source (NS):Transplant (NS) -1.5480 0.4133 -3.746 0.000647 ***


Supplemental Table 10B

(These model outputs are taken from the plasticity analysis and just constructed into tables here)

Table S10B. Linear model output assessing algal symbiont gene expression plasticity. The intercept was set at corals from the backreef transplanted back to the backreef. (BR = backreef, FR = forereef, NS = Nearshore)

Estimate Std. Error t value Pr(>t)
(Intercept) -1.2588 0.1355 -9.290 1.80e-10 ***
Source (FR) 1.7762 0.1916 9.270 1.90e-10 ***
Source (NS) 1.5797 0.2142 7.374 2.66e-08 ***
Transplant (FR) 1.5676 0.1916 8.181 3.06e-09 ***
Transplant (NS) 2.0990 0.2347 8.944 4.29e-10 ***
Source (FR):Transplant (FR) -2.9321 0.2710 -10.820 4.72e-12 ***
Source (NS):Transplant (FR) -1.0877 0.3030 -3.590 0.00112 **
Source (FR):Transplant (NS) NA NA NA NA
Source (NS):Transplant (NS) -3.0780 0.3319 -9.274 1.88e-10 ***


Final figures

Figure 1

Figure 1: Map of reef environments on the southern Belize Mesoamerican Barrier Reef System with in situ seawater temperatures recorded at these locations. (A) Model showing locations of forereef (FR; blue), backreef (BR; green), and nearshore (NS; orange) environments. Forereef and backreef sites are ~2-km apart on the seaward and landward sides of the Barrier Reef’s crest, respectively. The nearshore site is located 30-km west toward mainland Belize. (B) Mean (±1 SD) and distribution of in situ seawater temperatures taken every 30 minutes at forereef (blue), backreef (green), and nearshore (orange) environments from November 2014 to November 2015. (C) Weekly temperature ranges across the three reef environments demonstrating differences in temperature variability across sites.



Figure 2



Supplemental Figures

Figure S1

Figure S1. In situ temperatures recorded every 30 minutes from November 2014 to October 2015 on the nearshore (NS; orange), backreef (BR; green), and forereef (FR; blue) habitats assessed during this reciprocal transplant experiment on the Belize MBRS. (A) Raw temperature observations showing overall temperature patterns through the sampling period at each site. (B) Monthly, (C) Weekly, and (D) daily mean temperature comparisons across the three reef environments. (E) Monthly and (F) daily temperature ranges across the three reef environments demonstrating differences in temperature variability across sites.



Figure S2

Supplemental Figure 2. Calcification rate (mg cm–2 day–1) coloured by either (A-B) transplant or (C) source location (orange = NS [nearshore], green = BR [backreef], and blue = FR [forereef]), at (A, C) yearly intervals or (B) averaged over the entire transplant experimental period. Colored bars represent modeled 95% confidence intervals with corresponding raw calcification rates per colony denoted by circles of the same color.



Session Information:

Last run on 07 August 2023

## R version 3.6.3 (2020-02-29)
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